Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015012.1 Corchorus capsularis cultivar CVL-1 contig15033, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47885
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:6009 original size:7 final size:7
Alignment explanation
Indices: 5993--6035 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
5983 ATTGATTTTG
*
5993 TCTTCCT
1 TCTTCTT
6000 TCTTCTT
1 TCTTCTT
6007 TCTTCTT
1 TCTTCTT
6014 TCTTCTT
1 TCTTCTT
6021 TCTTCTT
1 TCTTCTT
6028 TCTTCTT
1 TCTTCTT
6035 T
1 T
6036 TTAAATGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (7 bp):
TCTTCTT
Found at i:14650 original size:55 final size:55
Alignment explanation
Indices: 14566--14676 Score: 197
Period size: 55 Copynumber: 2.0 Consensus size: 55
14556 TTAGTAGGAT
*
14566 TTGATGGTGACGAGGATTGGTCAAATGATGATAATATTCTCAATGATAAGCAGAC
1 TTGATGGTGACAAGGATTGGTCAAATGATGATAATATTCTCAATGATAAGCAGAC
14621 TTGATGGTGACAAGGA-TGGATCAAATGATGATAATATTCTCAATGATAAGCAGAC
1 TTGATGGTGACAAGGATTGG-TCAAATGATGATAATATTCTCAATGATAAGCAGAC
14676 T
1 T
14677 CATAGTCAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
54 3 0.06
55 51 0.94
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (55 bp):
TTGATGGTGACAAGGATTGGTCAAATGATGATAATATTCTCAATGATAAGCAGAC
Found at i:15438 original size:34 final size:34
Alignment explanation
Indices: 15399--15468 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
15389 TATAAGCTAA
* *
15399 ATTACATTGACAATGTATGGTATAATTATCCTAT
1 ATTACACTGACAATATATGGTATAATTATCCTAT
*
15433 ATTACACTGACGATATATGGTATAATTATCCTAT
1 ATTACACTGACAATATATGGTATAATTATCCTAT
15467 AT
1 AT
15469 ATAAAGCATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (34 bp):
ATTACACTGACAATATATGGTATAATTATCCTAT
Found at i:16819 original size:24 final size:24
Alignment explanation
Indices: 16787--16835 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
16777 ATCGGGACAA
*
16787 AGAGTTTGGGTCTTGATGGTCATG
1 AGAGTTTGGGTCCTGATGGTCATG
16811 AGAGTTTGGGTCCTGATGGTCATG
1 AGAGTTTGGGTCCTGATGGTCATG
16835 A
1 A
16836 TGTTCCATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.10, G:0.37, T:0.35
Consensus pattern (24 bp):
AGAGTTTGGGTCCTGATGGTCATG
Found at i:18297 original size:2 final size:2
Alignment explanation
Indices: 18290--18332 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
18280 ACGAAACATG
* *
18290 TA TA TA TA TA TA TA TA TA T- TA TA TA TC TA TA TC TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18330 TA T
1 TA T
18333 TAAAAAGTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:18314 original size:19 final size:19
Alignment explanation
Indices: 18290--18332 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
18280 ACGAAACATG
18290 TATATATATATATATATAT
1 TATATATATATATATATAT
* *
18309 TATATATCTATATCTATAT
1 TATATATATATATATATAT
18328 TATAT
1 TATAT
18333 TAAAAAGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATATATATATATATAT
Found at i:18827 original size:78 final size:78
Alignment explanation
Indices: 18737--18984 Score: 374
Period size: 78 Copynumber: 3.2 Consensus size: 78
18727 ATTGTTTAGG
* * ** *
18737 TTTTA-TAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAACA
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAACCTAATATCCTTATAACA
*
18801 ATTTTATTTTACCA
65 ATTATATTTTACCA
*
18815 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAAGCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAACCTAATATCCTTATAAC-A
*
18880 A-AATATTTTAACCA
65 ATTATATTTT-ACCA
*
18894 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAACCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAACCTAATATCCTTATAACAA
18959 TTATATTTTACCA
66 TTATATTTTACCA
18972 TTTTACTATTTTA
1 TTTTACTATTTTA
18985 ATTAAAAAAC
Statistics
Matches: 156, Mismatches: 10, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
78 79 0.51
79 77 0.49
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.48
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAACCTAATATCCTTATAACAA
TTATATTTTACCA
Found at i:18929 original size:79 final size:78
Alignment explanation
Indices: 18737--18984 Score: 374
Period size: 79 Copynumber: 3.2 Consensus size: 78
18727 ATTGTTTAGG
* * ** *
18737 TTTTA-TAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAAC-
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAACCTAATATCCTTATAACT
*
18800 AATTTTATTTTACCA
65 AA-TATATTTTACCA
*
18815 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAAGCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAACCTAATATCCTTATAACTA
*
18880 AAATATTTTAACCA
66 ATATATTTT-ACCA
18894 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAACCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAACCTAATATCCTTATAACTA
*
18959 TTATATTTTACCA
66 ATATATTTTACCA
18972 TTTTACTATTTTA
1 TTTTACTATTTTA
18985 ATTAAAAAAC
Statistics
Matches: 157, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
78 78 0.50
79 79 0.50
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.48
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAACCTAATATCCTTATAACTA
ATATATTTTACCA
Found at i:21740 original size:3 final size:3
Alignment explanation
Indices: 21732--21774 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
21722 AATATAAATA
*
21732 TAT TAT TAT TAT ATAT ATAT TAT TAT TGT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT -TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
21775 ATATATGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 27 0.75
4 7 0.19
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:21744 original size:17 final size:17
Alignment explanation
Indices: 21719--21758 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
21709 ATGTTGCCTA
*
21719 ATTAATATAAATATATT
1 ATTATTATAAATATATT
*
21736 ATTATTATATATATATT
1 ATTATTATAAATATATT
21753 ATTATT
1 ATTATT
21759 GTTATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTATAAATATATT
Found at i:21772 original size:17 final size:19
Alignment explanation
Indices: 21723--21774 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
21713 TGCCTAATTA
*
21723 ATATAAATATATTATTATT
1 ATATATATATATTATTATT
*
21742 ATATATATATTATTATTGTT
1 ATATATATA-TATTATTATT
21762 AT-TAT-TATATTAT
1 ATATATATATATTAT
21775 ATATATGAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 6 0.20
18 2 0.07
19 11 0.37
20 11 0.37
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATATATATATATTATTATT
Found at i:22620 original size:31 final size:31
Alignment explanation
Indices: 22575--22643 Score: 122
Period size: 31 Copynumber: 2.2 Consensus size: 31
22565 GCACGGGATA
22575 TGTTCATTTTAATATTTAGGTAATGATCAATG
1 TGTTCA-TTTAATATTTAGGTAATGATCAATG
22607 TGTTCATTTAATATTTAGGTAATGATCAATG
1 TGTTCATTTAATATTTAGGTAATGATCAATG
22638 T-TTCAT
1 TGTTCAT
22644 ATTTGGACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 5 0.14
31 26 0.70
32 6 0.16
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.48
Consensus pattern (31 bp):
TGTTCATTTAATATTTAGGTAATGATCAATG
Found at i:31838 original size:8 final size:8
Alignment explanation
Indices: 31825--31883 Score: 57
Period size: 8 Copynumber: 6.9 Consensus size: 8
31815 TTTCCATCAC
31825 TCTTTTTT
1 TCTTTTTT
31833 TCTTTTTT
1 TCTTTTTT
*
31841 TCTTTTCT
1 TCTTTTTT
31849 TCTTTTTCAATT
1 TC-TTTT---TT
31861 TCTTTTTCT
1 TCTTTTT-T
31870 TCTTTTTT
1 TCTTTTTT
31878 T-TTTTT
1 TCTTTTT
31884 AATTTCTTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
7 5 0.11
8 20 0.45
9 12 0.27
11 4 0.09
12 3 0.07
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.81
Consensus pattern (8 bp):
TCTTTTTT
Found at i:31849 original size:21 final size:21
Alignment explanation
Indices: 31825--31903 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
31815 TTTCCATCAC
31825 TCTT-TTTTTCTTTTTTTCTTT
1 TCTTCTTTTTCTTTTTTT-TTT
** *
31846 TCTTCTTTTTCAATTTCTTTT
1 TCTTCTTTTTCTTTTTTTTTT
*
31867 TCTTCTTTTT-TTTTTTTAATT
1 TCTTCTTTTTCTTTTTTT-TTT
**
31888 TCTTCTTCATCTTTTT
1 TCTTCTTTTTCTTTTT
31904 GAGGTGGGTA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 4 0.09
21 27 0.59
22 15 0.33
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (21 bp):
TCTTCTTTTTCTTTTTTTTTT
Found at i:31856 original size:38 final size:37
Alignment explanation
Indices: 31805--31883 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
31795 TGATTTGATT
* *
31805 TTTTGTTCATTTTCCATCACTCTTTTT-TTCTTTTTTTC
1 TTTTCTTCATTTTCAAT--CTCTTTTTCTTCTTTTTTTC
* * *
31843 TTTTCTTCTTTTTCAATTTCTTTTTCTTCTTTTTTTT
1 TTTTCTTCATTTTCAATCTCTTTTTCTTCTTTTTTTC
31880 TTTT
1 TTTT
31884 AATTTCTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
36 7 0.20
37 14 0.40
38 14 0.40
ACGTcount: A:0.06, C:0.18, G:0.01, T:0.75
Consensus pattern (37 bp):
TTTTCTTCATTTTCAATCTCTTTTTCTTCTTTTTTTC
Found at i:31881 original size:27 final size:28
Alignment explanation
Indices: 31831--31903 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
31821 TCACTCTTTT
31831 TTTCTTTTT-TTCTTTTCTTCTTTTTCAA
1 TTTCTTTTTCTTCTTTT-TTCTTTTTCAA
*
31859 TTTCTTTTTCTTCTTTTTT-TTTTTTAA
1 TTTCTTTTTCTTCTTTTTTCTTTTTCAA
* *
31886 TTTCTTCTTCATCTTTTT
1 TTTCTTTTTCTTCTTTTT
31904 GAGGTGGGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 23 0.56
28 11 0.27
29 7 0.17
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTCTTTTTCTTCTTTTTTCTTTTTCAA
Found at i:39920 original size:202 final size:203
Alignment explanation
Indices: 39542--40365 Score: 1334
Period size: 202 Copynumber: 4.0 Consensus size: 203
39532 TTTTGTGTCA
* *
39542 TATCAAACCTTATACAAGTAAAAACAATCCCGCATATAACTAATAAACATGTCTTAGAATTCAAA
1 TATCAAACC-T-TACAAGTAAAAACAATCCCGCATATAGCTAATAAACACGTCTTAGAATTC-AA
* * * *
39607 AAAAAAAAATGGTGTGGTGCTCTGCATGGCTGACTTATGGCACATGTTTATTTTTTTTTTACACA
63 AAAAAAAAATGGTGTGGTACTCTGCATGGCTGACTTATGGCACATATTTA-TTTTTTTTGACACC
* *
39672 TGTTTTATTTTGTTAGGTCGGGTTATCTCTAGTACATAAATTTAAATCTATGTGGAGTAATAAAT
127 TGTTTTATTTTGTTGGGCCGGGTTATCTCTAGTACATAAATTTAAATCTATGTGGAGTAATAAAT
39737 ATAGGATTTTTC
192 ATAGGATTTTTC
*
39749 TATCAAACCTTACAAGTAAAACCAATCCCGCATATAGCTAATAAACACGTCTTAGAATTCAAAAA
1 TATCAAACCTTACAAGTAAAAACAATCCCGCATATAGCTAATAAACACGTCTTAGAATTCAAAAA
*
39814 AAAAAATGGTGTGGTGCTCTGCATGGCTGACTTATGGCACATATTTA-TTTTTTTGACACCTGTT
66 AAAAAATGGTGTGGTACTCTGCATGGCTGACTTATGGCACATATTTATTTTTTTTGACACCTGTT
*
39878 TTATTTTGTTGGGCCGGGTTATCTCTAGCACATAAATTTAAATCTATGTGGAGTAATAAATATAG
131 TTATTTTGTTGGGCCGGGTTATCTCTAGTACATAAATTTAAATCTATGTGGAGTAATAAATATAG
39943 GATTTTTC
196 GATTTTTC
*
39951 TATCAAACCTTACAAGTAAAAACAATCTCGCATATAGCTAATAAACACGTCTTAGAATTC--AAA
1 TATCAAACCTTACAAGTAAAAACAATCCCGCATATAGCTAATAAACACGTCTTAGAATTCAAAAA
* *
40014 TAAAAATGGTGTGGTACTCTGCATGGCTGACTTATGGCACATGTTT-TTTTTTTTGACACCTGTT
66 AAAAAATGGTGTGGTACTCTGCATGGCTGACTTATGGCACATATTTATTTTTTTTGACACCTGTT
*
40078 TTATTTTGTTGGGCCGGGTT-TCTCTAGTACATGAATTTAAATCTATGTGGAGTAATAAATATAG
131 TTATTTTGTTGGGCCGGGTTATCTCTAGTACATAAATTTAAATCTATGTGGAGTAATAAATATAG
40142 GATTTTTC
196 GATTTTTC
*
40150 TATCAAACCGTACAAGTAAAAACAATCCCGCATATAGCTAATAAACAACGTCTTAAGAATTCAAA
1 TATCAAACCTTACAAGTAAAAACAATCCCGCATATAGCTAATAAAC-ACGTCTT-AGAATTCAAA
*
40215 TAAAAAAATGGTGTGGTACTCTGCATGGCTGACTTATGGCACATGTTTATTTTTTATTTTTTTTG
64 AAAAAAAATGGTGTGGTACTCTGCATGGCTGACTTATGGCACA----TA---TTTATTTTTTTTG
*
40280 ACACCTGTTTTATTTTGTTGGGCCGGGTTATCTCTAGTACATAAATTTAAATCTATATGGAGTAA
122 ACACCTGTTTTATTTTGTTGGGCCGGGTTATCTCTAGTACATAAATTTAAATCTATGTGGAGTAA
40345 TAAATATAGGATTTTTC
187 TAAATATAGGATTTTTC
40362 TATC
1 TATC
40366 TTTTATTTCT
Statistics
Matches: 580, Mismatches: 23, Indels: 23
0.93 0.04 0.04
Matches are distributed among these distances:
199 94 0.16
200 90 0.16
201 7 0.01
202 143 0.25
203 42 0.07
204 51 0.09
205 47 0.08
206 1 0.00
207 10 0.02
210 3 0.01
211 38 0.07
212 54 0.09
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (203 bp):
TATCAAACCTTACAAGTAAAAACAATCCCGCATATAGCTAATAAACACGTCTTAGAATTCAAAAA
AAAAAATGGTGTGGTACTCTGCATGGCTGACTTATGGCACATATTTATTTTTTTTGACACCTGTT
TTATTTTGTTGGGCCGGGTTATCTCTAGTACATAAATTTAAATCTATGTGGAGTAATAAATATAG
GATTTTTC
Found at i:44195 original size:15 final size:15
Alignment explanation
Indices: 44164--44284 Score: 91
Period size: 13 Copynumber: 8.5 Consensus size: 15
44154 TATAAAAGTA
*
44164 AATATATATTTATTAT
1 AATATATA-TAATTAT
44180 AATATATATAATTAT
1 AATATATATAATTAT
*
44195 AATTTATATAA-TA-
1 AATATATATAATTAT
*
44208 AATATATAGAA--AGT
1 AATATATATAATTA-T
44222 AA-ATATATAATTACT
1 AATATATATAATTA-T
*
44237 -CTATATAT-ATTAT
1 AATATATATAATTAT
*
44250 -ATATATA-AAGTA-
1 AATATATATAATTAT
*
44262 AATACATATAATTAT
1 AATATATATAATTAT
44277 AATATATA
1 AATATATA
44285 ATTTATATTT
Statistics
Matches: 84, Mismatches: 12, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
12 1 0.01
13 32 0.38
14 12 0.14
15 31 0.37
16 8 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
AATATATATAATTAT
Found at i:44204 original size:24 final size:26
Alignment explanation
Indices: 44166--44213 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
44156 TAAAAGTAAA
*
44166 TATATATTTATTATAATATATATAAT
1 TATATATTTATTATAATAAATATAAT
44192 TATA-ATTTA-TATAATAAATATA
1 TATATATTTATTATAATAAATATA
44214 TAGAAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.57
25 5 0.24
26 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TATATATTTATTATAATAAATATAAT
Found at i:44282 original size:39 final size:39
Alignment explanation
Indices: 44180--44292 Score: 115
Period size: 39 Copynumber: 2.8 Consensus size: 39
44170 TATTTATTAT
*
44180 AATATATATAATTATAATTTATATAATAAATATATAGAAAGTA
1 AATA-ATATAATTATAA--TATATAAT-TATATATAGAAAGTA
* *
44223 AAT-ATATAATTACT-CTATATATATTATATATATAAAGTA
1 AATAATATAATTA-TAATATATA-ATTATATATAGAAAGTA
44262 AATACATATAATTATAATATATAATT-TATAT
1 AATA-ATATAATTATAATATATAATTATATAT
44293 TTATTATTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
39 27 0.44
40 6 0.10
41 24 0.39
42 1 0.02
43 3 0.05
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (39 bp):
AATAATATAATTATAATATATAATTATATATAGAAAGTA
Found at i:44283 original size:41 final size:40
Alignment explanation
Indices: 44180--44292 Score: 117
Period size: 41 Copynumber: 2.8 Consensus size: 40
44170 TATTTATTAT
* *
44180 AATATATATAATTATAATTTATATAATAAATATATAGAAAGTA
1 AATA-ATATAATTATAATATATAT-AT-TATATATAGAAAGTA
* *
44223 AAT-ATATAATTACT-CTATATATATTATATATATAAAGTA
1 AATAATATAATTA-TAATATATATATTATATATAGAAAGTA
44262 AATACATATAATTATAATATATA-ATT-TATAT
1 AATA-ATATAATTATAATATATATATTATATAT
44293 TTATTATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
39 21 0.34
40 6 0.10
41 30 0.49
42 1 0.02
43 3 0.05
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (40 bp):
AATAATATAATTATAATATATATATTATATATAGAAAGTA
Found at i:44597 original size:25 final size:25
Alignment explanation
Indices: 44547--44596 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
44537 AACAACTACT
44547 TCCCACTTTGATTATTTTTTGAAAAA
1 TCCCACTTTGATTA-TTTTTGAAAAA
44573 TCCCACTTTGATTA-TTTTGAAAAA
1 TCCCACTTTGATTATTTTTGAAAAA
44597 AAAAAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 10 0.42
26 14 0.58
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (25 bp):
TCCCACTTTGATTATTTTTGAAAAA
Done.